Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010508.1 Corchorus olitorius cultivar O-4 contig10540, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 8772
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33


Found at i:33 original size:2 final size:2

Alignment explanation


    Indices: 28--55  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

         18 TGTGTGTGTG

                                                     
         28 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

         56 GTTGAATGAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:4361 original size:162 final size:162

Alignment explanation


    Indices: 4094--4492  Score: 649
    Period size: 162  Copynumber: 2.5  Consensus size: 162

       4084 AATGCGGATC

                            *           *                                    
       4094 ATGACCAAACTTTGCAGGACTTCTTTCACAATGTTCATAAGCATATCACCATCTTCATGGAGCCA
          1 ATGACCAAACTTTGCAAGACTTCTTTCATAATGTTCATAAGCATATCACCATCTTCATGGAGCCA

               *      *                                 *                    
       4159 TTTTCACGCTTAAATCTTCCTATTCTGGTGTTTTGTCCTTAACTGAAAACCGAGTAAAAGTTACG
         66 TTTCCACGCTCAAATCTTCCTATTCTGGTGTTTTGTCCTTAACTAAAAACCGAGTAAAAGTTACG

            *                   *           
       4224 TTCTGCACCAGAATGAGTCAGAATTTGTGGAA
        131 CTCTGCACCAGAATGAGTCAAAATTTGTGGAA

                                                                             
       4256 ATGACCAAACTTTGCAAGACTTCTTTCATAATGTTCATAAGCATATCACCATCTTCATGGAGCCA
          1 ATGACCAAACTTTGCAAGACTTCTTTCATAATGTTCATAAGCATATCACCATCTTCATGGAGCCA

                                                                             
       4321 TTTCCACGCTCAAATCTTCCTATTCTGGTGTTTTGTCCTTAACTAAAAACCGAGTAAAAGTTACG
         66 TTTCCACGCTCAAATCTTCCTATTCTGGTGTTTTGTCCTTAACTAAAAACCGAGTAAAAGTTACG

                   * *                      
       4386 CTCTGCATCGGAATGAGTCAAAATTTGTGGAA
        131 CTCTGCACCAGAATGAGTCAAAATTTGTGGAA

                          *  *                         *                   * 
       4418 ATGGACCAAACTTTTCACGACTTCTTTCACT-ATGTTCATAAGAATATCACCATCTTCAT-GATC
          1 AT-GACCAAACTTTGCAAGACTTCTTTCA-TAATGTTCATAAGCATATCACCATCTTCATGGAGC

                        
       4481 CATTTCCACGCT
         64 CATTTCCACGCT

       4493 GGTGTTTTGT


Statistics
Matches: 222,  Mismatches: 13, Indels: 4
        0.93            0.05        0.02

Matches are distributed among these distances:
 162  170  0.77
 163   51  0.23
 164    1  0.00

ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33


Consensus pattern (162 bp):   
ATGACCAAACTTTGCAAGACTTCTTTCATAATGTTCATAAGCATATCACCATCTTCATGGAGCCA
TTTCCACGCTCAAATCTTCCTATTCTGGTGTTTTGTCCTTAACTAAAAACCGAGTAAAAGTTACG
CTCTGCACCAGAATGAGTCAAAATTTGTGGAA

Found at i:8515 original size:2 final size:2

Alignment explanation


    Indices: 8508--8532  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       8498 ATTATGTATA

                                                 
       8508 TG TG TG TG TG TG TG TG TG TG TG TG T
          1 TG TG TG TG TG TG TG TG TG TG TG TG T

       8533 ATATATATAT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52


Consensus pattern (2 bp):   
TG

Found at i:8537 original size:2 final size:2

Alignment explanation


    Indices: 8532--8556  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       8522 TGTGTGTGTG

                                                 
       8532 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

       8557 GTTGAATGAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Done.